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Structure of mature activin A with small molecule 42
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ARV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 291 1.65 M (NH4)2SO4, 4 % PEG 300, 100 mM Hepes pH 7.4, 2 % DMSO
Crystal Properties Matthews coefficient Solvent content 3.57 65.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.05 α = 90 b = 96.938 β = 90 c = 117.242 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.97859 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.04 74.71 97.2 0.194 0.206 0.069 0.997 8.7 8.6 23146
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.15 100 2.894 3.068 1.008 0.487 8.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2arv 2.04 74.71 21896 1118 96.68 0.2248 0.2233 0.237 0.254 0.2623 RANDOM 54.307
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -2.86 -1.02 3.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.268 r_dihedral_angle_4_deg 24.529 r_dihedral_angle_3_deg 20.137 r_dihedral_angle_1_deg 8.448 r_angle_refined_deg 2.165 r_angle_other_deg 1.165 r_chiral_restr 0.13 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.268 r_dihedral_angle_4_deg 24.529 r_dihedral_angle_3_deg 20.137 r_dihedral_angle_1_deg 8.448 r_angle_refined_deg 2.165 r_angle_other_deg 1.165 r_chiral_restr 0.13 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1775 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing